Btw, Avara, just a few suggestions.
While I agree that implementing the PokeDex in an ancient era makes no sense, I still think there should be SOME substitute for it which allows trainers to still get interesting info on the Pokemon, such as their habitat(s) for one. Maybe there could be a journal where the Pokemon's pictures and information can be posted and obtained. A game without the PokeDex or a suitable replacement, I dunno, feels off - but hey, it's your hack, do what you want. Another suggestion involves music, and I'd say getting music from games like Legend of Zelda (basically, those that take place in a hypothetical medieval era and world) would be a good idea. This is something you can implement later.
I also think that even if you won't implement Potions ingame, there can still be some medicines (maybe herbal remedies or magical tonics/elixirs) that could take their place. Either that, or you can change the Berries' own properties (particularly the ones that are either meant to be turned into PokeBlocks or already restore HP) so they can replace Potions more effectively. For example, turn the Bluk Berry (PokeBlock berry) into a Revive, or turn Watmel Berry (another PokeBlock berry IIRC) into a Full Restore. It would be quite helpful for people playing the game. Last but not least, do the two heroes get their starters already evolved, or in their base states? Because evolved starters could make the game quite a bit unbalanced in their favor.
Again, best of luck with your hack! It looks pretty sweet and can be awesome if you do it right.